PTCD2

pentatricopeptide repeat domain 2, the group of Pentatricopeptide repeat containing

Basic information

Region (hg38): 5:72320367-72368395

Links

ENSG00000049883 ∙ NCBI:79810 ∙ OMIM:615484 ∙ HGNC:25734 ∙ Uniprot:Q8WV60 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PTCD2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PTCD2 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			29	3		32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	3	0

Variants in PTCD2

This is a list of pathogenic ClinVar variants found in the PTCD2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
5-72320414-G-T		not specified	Uncertain significance (Jan 09, 2024)
5-72320417-C-G		not specified	Uncertain significance (Sep 27, 2024)
5-72320447-A-C		not specified	Uncertain significance (Aug 11, 2022)
5-72320483-C-T		not specified	Uncertain significance (May 27, 2022)
5-72322181-A-T		not specified	Uncertain significance (Dec 06, 2022)
5-72326635-A-G		not specified	Likely benign (Nov 29, 2023)
5-72326647-C-A		not specified	Uncertain significance (Jan 08, 2025)
5-72326667-G-C		not specified	Uncertain significance (Feb 28, 2023)
5-72326681-C-T		not specified	Uncertain significance (Feb 15, 2025)
5-72326704-C-T		not specified	Uncertain significance (Dec 17, 2023)
5-72326716-G-A		not specified	Uncertain significance (Aug 12, 2024)
5-72331294-G-C		not specified	Uncertain significance (Apr 17, 2024)
5-72331308-C-T		not specified	Uncertain significance (Jul 08, 2022)
5-72331340-C-G		not specified	Uncertain significance (Jun 18, 2021)
5-72335049-C-T		not specified	Uncertain significance (Apr 22, 2024)
5-72335057-A-G		not specified	Uncertain significance (Aug 11, 2024)
5-72335819-G-T		not specified	Uncertain significance (Jan 16, 2024)
5-72335854-A-G		not specified	Uncertain significance (Nov 12, 2024)
5-72335877-T-C		not specified	Uncertain significance (Jun 29, 2023)
5-72338650-C-G		not specified	Uncertain significance (Oct 21, 2024)
5-72338659-G-A		not specified	Uncertain significance (Sep 12, 2024)
5-72338697-A-G		not specified	Uncertain significance (Mar 14, 2023)
5-72338698-G-C		not specified	Uncertain significance (Aug 16, 2022)
5-72342980-G-A		not specified	Likely benign (Dec 17, 2023)
5-72343022-T-G		not specified	Uncertain significance (May 26, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PTCD2	protein_coding	protein_coding	ENST00000380639	10	39859

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.13e-11	0.135	125677	0	71	125748	0.000282

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.128	196	201	0.975	0.00000968	2543
Missense in Polyphen		33	44.557	0.74062		604
Synonymous	-0.750	88	79.5	1.11	0.00000403	733
Loss of Function	0.503	17	19.4	0.877	9.19e-7	260

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000931	0.000929
Ashkenazi Jewish	0.00	0.00
East Asian	0.000385	0.000381
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000204	0.000202
Middle Eastern	0.000385	0.000381
South Asian	0.000362	0.000359
Other	0.000330	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in mitochondrial RNA maturation and mitochondrial respiratory chain function. {ECO:0000250}.

Intolerance Scores

• loftool: 0.695
• rvis_EVS: -0.65
• rvis_percentile_EVS: 16.36

Haploinsufficiency Scores

• pHI: 0.0276
• hipred: N
• hipred_score: 0.144
• ghis: 0.560

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.246

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Ptcd2
• Phenotype: liver/biliary system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); renal/urinary system phenotype; muscle phenotype; cellular phenotype

Gene ontology

• Biological process: kidney development;liver development;mRNA processing;mitochondrion organization;muscle fiber development;regulation of mRNA processing;ventricular cardiac muscle tissue morphogenesis
• Cellular component: mitochondrion
• Molecular function: RNA binding